Run
by C.W. Smith
Summary: Sometimes the only thing you can do to protect what you love is run.
1. Homecoming

Run

Chapter 1: Homecoming

An Evangelion Fanfiction

By: LD

Disclaimer: I do not own Evangelion. That's all that has to be said.

"It'll be alright baby," he said as he held the small child in his arms. They had been on the run for what felt like forever, but had actually been only a month. Only brief hours of rest had been granted to the pair as they ran, him looking over his shoulder at every turn. Had it been only him he'd probably not have been concerned, but his daughter meant too much to him to even risk being taken from her. He could only hope that the few people he knew all those years ago would still be around and help him in his time of need.

It was ironic, but after ten years the city that had destroyed all his hopes was now the last hope he and his daughter had. He couldn't rest until his daughter was safe from whoever sought them. He thought about her mother, how they had met on the run from different things. Him from his past, and her from something dark she couldn't risk telling even him. She had always said they would come after him if they thought she had told them anything.

Now he couldn't be certain if they did, or if they were still after them. He was good at disappearing, he had done it well over the years from friends and family. Now, he carried his daughter and ran for their lives. She hadn't known any peace since this had started again. She was terrified, he could see that in his daughter's once bright green eyes now clouded in terror.

He saw the sign as it passed the train, the city of his lost and last hope. How fitting he should have to return here, this city where even Angels feared to tread. The young girl had also seen the sign and asked, "Will we be safe from the bad people here?"

"I hope so Mana, I hope so," he said. All he could do was hope and hold his daughter tighter. After ten long years full of darkness, light, pain, and joy Shinji Ikari had returned to the accursed city of Tokyo-3

--

One look at the calender was all she needed to tell her this was going to be a lousy day. Ten years to the day, Third Impact had been stopped by one boy. She had known him, and blamed herself for much of the agony he had gone through. One look in the mirror reminded her of the nightmares they had both seen and went through.

Later that night, there would be a memorial at NERV Central command. They would remember those lost during the war and the invasion. Lost friends, and scars that would never heal. The same thing they had done every year since the end of the war. And she was still working for them. Hell, THEY were still working for them. He roommate had had just as rough a time during the war as he had.

Slowly, she ran a brush through her all too quickly graying hair. Another sign of the times. She looked ten years older then she should because of what had happened. The hair at her temples slowly turning from the vibrant colors of youth to the iron of old age. Perhaps that was for the best. Now that she saw herself in the mirror, Misato Katsuragi wondered exactly how much she'd have to drink before she wouldn't be able to see herself in there again.

Probably more then her body could take these days. She couldn't even drink Asuka under the table anymore. It made Misato happy though, that after all these years Asuka was still her roommate at the apartment. It had been a wild party when Asuka had come of age though. That had been when she ceased being Misato's Child and became the older womans drinking buddy and confidant.

But on this day, they both preferred a more subdued activity. They would each pour one glass of sake, and toast the boy who had rounded out the patch-work family. Neither of them knew what had happened to Shinji, he had just disappeared. They probably would never know unless he came back, and even then... Misato didn't know what would happen if that day came. She just hoped that somehow he had found some peace and happiness in the last decade.

"Misato, hurry up! We're going to be late!" Asuka yelled from the kitchen.

"I'm coming!"

--

"Do you think Shinji finally found something to make him happy?" Asuka asked thoughtfully. The two of them had had this conversation before. Many times in fact as Asuka had worked through her recovery from the physical and psychological injures the war had inflicted on her. The doctors had said it was healthy for her to think about it. The reason being that much of her issues centered around the Third Child.

"It's been ten years, I like to think he did. Even if it wasn't with us, he earned at least some peace," Misato answered. She always gave the same answer.

Asuka rolled her eyes at the older woman. She never went any deeper into her thoughts about the Third. Asuka however knew she sometimes dwelt too much on the subject. It had been why she hadn't had a relationship that lasted longer then a month. She compared each man she dated with a boy she had known at fourteen. It didn't make sense really, neither of them had been very mature. She understood this now that she had years to reflect on it. It wasn't that she had that might have been feeling. She just wanted to have a chance to make amends for how she had been at the time.

Of course, it hadn't been like they had given him any reasons to stay after the war. He disappeared shortly after the final battle, probably believing Misato and her were dead. It of course was almost divine providence that they had survived. The scars were still there though, Misato's gunshot wound and a few scars around her left eye. But time and some plastic surgery had helped the scar fade.

She kept thinking of Shinji and what he might be doing at the moment as the car began the long decent into the hole that used to be the Geofront.

--

It was extremely busy as the train stopped at the station. Shinji carried his small daughter off the train in one arm, as he carried their meager belongings in the other hand. They hadn't been able to take much with them, just some clothes for him and Mana. Also in the bag was their only possession that was worth anything to them, their photo album. They wanted to keep that especially, as it had the only pictures they had ever taken of Mana's mother.

Mana clung to him tightly as the people heading out to the suburbs from their work day surrounded them. He knew she was scared because of everything they had went through the past month. He was scared to, but kept up a brave face for his little girl. He would die before letting anything happen to her. Shinji had promised himself when she was born that no matter what he would be there for her.

He walked over to one of the many pay phones at the terminal. He set Mana down on the ground so he could make the call he needed to make. The small child just clung to her fathers leg, afraid to let go or even risk being separated from him. She looked up and saw him talking into the phone, then hang up. Shinji picked Mana back up then carried her over to one of the benches on the terminal. There was still a lot of activity at the train station, providing them with some security as people went about their business.

"I'm tired, Papa," Mana said quietly.

Shinji pulled her into his lap and held her tight, "Go ahead and rest baby, I'll keep you safe while you sleep."

--

"Well, if it isn't the two most lovely women in NERV," came a friendly voice from down the corridor. Both women recognized it, and Asuka chuckled as Misato's expression soured. They still acted like children around each other, even after all they had been through. Asuka still didn't know quiet what Kaji had done before the Fifteenth Angel, but aside from that she was happy he was still around. Asuka knew that for all her denials, Misato was glad he was around as well.

"Well, good to see you 'Old Man'," Asuka said with a smile.

"If I were a few years younger we'd see if you thought that," Kaji said, turning his charm on full.

"Nice try, lover boy, but you wouldn't stand up to my expectations," Asuka countered.

They both smirked at each other as Misato's face turned red. It was too much for either of them as the broke down laughing at the woman. The glare she cast at them however could have melted Evangelion Armor.

Kaji spoke up before Misato could blow, "It's that time again. Every year things around here get so depressed. Not that there isn't any reason for it."

Misato calmed, "At least we're around to remember why it does."

The trio began walking towards the command bridge, all three lost in thought and reflection. Something thought kept Kaji's mind on things other then lost friends. One of his contacts had informed him of a possible fugitive from the JSSDF heading for Tokyo-3. He hadn't gotten anything other then the man was running and had a young girl with him. Most likely that was his daughter as the contact stated they had been monitoring him for sometime. There was no identity given to the fugitive, Kaji had just been asked to keep an eye out on any NERV intel that would lead to his apprehension. Kaji of course kept it close to his vest. If the fugitive was running from the military then he might know something Kaji would like to know himself.

They entered the Command bridge, finding everyone at their stations. Makato and Shingru both dutifully remained on the bridge, Makato still Misato's top aide. They had all been promoted twice since the end of the war, but were happy to remain where they were. Maya had been made the head of Section-1 after Ritsuko had died.

And sitting at the command chair was Commander Gendo Ikari, probably the only man Misato and Asuka felt should have been dead. Somehow he had escaped imprisonment after the investigation into Third Impact. But he hadn't come out completely unscathed himself. The lose of his hand had never been explained to the public or anyone else. The proof however was easily identified, as now he had one white glove, and one cybernetic prosthetic that was encased in black latex.

He had mellowed though over the years. For some reason after the impact he had become more outgoing with the rest of the staff. He had shed the stone from his visage and shaved the beard that he had been known for. Fuyutsuki had once mentioned to Misato in passing, that Commander Ikari now resembled the brash college student he had bailed out of jail once. Not the cold unfeeling commander, that everyone feared.

Commander Ikari stood from his desk and spoke, "Attention."

Everyone stood from their stations, turning and facing the command chair. It had been the same ritual every year. The Commander would call the room to attention, say a few words, and then everything would come to an end. Same as always, routine remembrances of the fallen.

This year however Shingru's console went off, indicating something requiring his immediate attention. Shortly after that the alert siren for the facility began going off. Immediately both Shingru and Makato were at their stations pulling down status reports. The phone next to Shingru's station went off.

The long haired tech answered the phone, "Command, go ahead. Are you certain? Has there been confirmation?"

"Captain, report," Misato ordered.

"We just got a call on the emergency line. The caller gave a valid NERV emergency code to the operator."

"What's the code?" Commander Ikari asked.

"Code... Code is_ Alpha-Zulu-six-eight-__niner_," he answered with disbelief in his voice.

"That's a pilot in distress code," Asuka said, confused.

The look on Misato's face though said it was more then that, "That's not just any distress code. I want confirmation from MAGI authenticating this code. Makato, trace the call to it's point of origin. I want to know where it came from, and I want to know ninety seconds ago!"

Maya ran the code through the MAGI and the voice print as Makato worked on the trace. Maya was done first, "MAGI confirms and authenticates distress code. Bringing up the pilot profile for the code now."

When the information was displayed on the vast holographic monitor it confirmed Misato's thoughts. She could hear Asuka gasp behind her, even Kaji muttering, "My God."

The code belonged to Pilot Shinji Ikari. Misato turned to the Commander, and saw him speaking to Fuyutsuki just so no one could hear them.

"So, he's come back after all this time," Fuytusuki said.

"He wouldn't use an emergency code just to make contact with Katsuragi or Soryu. Even if he didn't know where they were he'd look for them and try to keep off our radar," Gendo mused. He had changed over the last few years, the regrets of his past weighing on him. He turned quickly and looked directly at Misato.

"Colonel Katsuragi, I want you to make personal contact. Get moving, we'll relay the location to you when we have it," Ikari ordered.

"Yes sir. Asuka, with me!" Misato said as she ran off the bridge, Asuka on her heels the whole way.

Gendo walked down from his desk now stood right behind the bridge crew. Several reasons floated through his head as to why his son would return to this city. Most of them he cast out of hand, as they wouldn't have pushed him to calling NERV at all. Other possible scenarios went through his mind, the most likely of which was that he was in trouble. Even then Shinji wouldn't have dialed a number telling him where he was. Unless... he was trying to protect something, or someone.

"Sir, we have a lock on the call. Call originated at transit station L3 in the Tokai district," Makato reported.

"Relay the location to Colonel Katsuragi. How many Section-2 agents do we have in and around that station?"

"Three conducting routine surveillance in the station itself, and seven others in the surrounding area on patrol," Shingru said.

"I want all agents in the area diverted to the perimeter of the station. Are there any agents in the station that could make a positive identification?"

"One, Agent Kensuke Aida. He went to school with Pilot Ikari during the war. If anyone could confirm it would be him," Makato reported.

"Very well, patch me through to him," the Commander ordered.

--

Misato slammed the gas and tore out in the direction of the station as soon as the gate for the car train had opened. Asuka held on for dear life as Misato's driving was erratic. Asuka checked both their sidearms as they went. She and Misato had come to the same conclusion Gendo had.

"What sort of mess has he gotten himself into this time?" Asuka asked absently.

"Don't know, but it must be big if he'd even think about coming back after all this time," Misato answered.

"You think he expects us to help him?"

"As if we wouldn't, this is Shinji we're talking about here. No, I don't believe he's thinking about anything other then protecting whatever it is he's got with him," Misato said, focused on the road as she avoided the traffic.

"What do you think he would be protecting?" Asuka asked.

"No idea, but it is obviously pretty important to him."

--

It had been a relatively quiet day for Kensuke. Masquerading as a janitor in a transit station wasn't exactly his idea of a good assignment. But it did give him a chance to watch the comings and goings of people. One odd couple he had seen leave the train earlier was still sitting at the same bench they had set down at for the past few minutes. A young man and child huddled together as the people passed by. Just watching them broke his heart, he could tell they had lost a lot before getting here. The man looked horribly familiar to Kensuke as well, as if he had seen him before.

Before Ken could run through his memory, the communication device hidden in his ear went off. He went to the janitorial closet and closed the door, giving the appearance to the rest of the world that he was simply getting more cleaning supplies for his duties.

"Aida online," he said into the receiver in his collar.

"Agent Aida, this is Commander Ikari."

The commander himself? Something must have been up if Ikari was contacting a lowly agent.

"Sir."

"We've just received a PID code from your location. MAGI confirms the code belongs to Pilot Shinji Ikari. Katsuragi and Soryu are on their way to your location now, eta five minutes. Can you give us a visual confirmation," the Commander said.

So that's why that man looked familiar, he should have put it together long before now. If he had not been on the line he would have smacked himself in the head. He responded to the Commander quickly, "That's an affirmative sir. He came off the train about an hour ago, made a phone call, and is now sitting at one of the benches with a small girl, probably three or four years old."

"You said a young girl, Agent Aida?"

"Yes sir."

--

The Commander added that piece of information into his thoughts as he evaluated the situation. Fuyutsuki came up behind him and voiced what Ikari was already thinking, "Well, we know what he's protecting now. Now the question becomes what's he protecting her from?"

"Or whom," Ikari said.

"Sir, did you dispatch additional agents to this station?" Kensuke asked.

"Negative, no additional agents were dispatched," Gendo said. He could already guess why the young agent had asked.

"Then we have a problem. I have five, repeat five Section-2 agents entering the facility. I don't recognize any of them, but I haven't met every agent on the roster. Orders sir?"

"Proceed on your own discretion, we'll send additional support to your location. They should be there in two minutes," Gendo ordered.

"Understood sir, Aida out," Kensuke signed off his radio and then started removing the jumpsuit he had been wearing as his disguise. underneath he wore his customary button up shirt and black slacks. He pulled his radio back out and contacted the two men he was working with that day.

"Sadatmo, Anno, come in."

"Here," Agent Sadatmo answered.

"Online," Came Anno's voice.

"We have five hostiles in the terminal, black suits, ear wires, the works. Commander Ikari has given orders that they are not to be allowed to intercept the Adult male and young female at the bench near the Kyoto line. Male is identified as Shinji Ikari, the child is unknown," Kensuke relaied to his compatriots.

"So what is our plan?" Anno asked.

"I'm going to make contact with Ikari. We went to school together, my popping up on the way home won't look too suspicious. Anno, swing around to the left, Sadatmo to the right. If this turns into a fire fight I want to get these guys boxed in."

"Roger," Sadatmo responded.

"Good to go," Anno said.

Kensuke pulled the jump suit he had been wearing off, revealing a white business shirt and black slacks. He tossed on his sports jacket and a tie, making sure it was loosened enough to look like he had finished a hard day of number crunching. Stepping out into the platform he threw his jacket over his shoulder. Kensuke tried to look as natural as he could, which wasn't too hard. He had done this same thing every day when returning home from NERV.

Kensuke had walked up to the ticket counter and purchased one ticket. He went to a point in the terminal where he could see Shinji, and then stood there. The crowd had thinned out as the evening rush ended, leaving only a few civilians in the area. Four of the five agents he had seen had dispersed themselves at the entrances. Ken hoped Misato and Asuka had been briefed on what was happening.

The fifth was walking towards Shinji. Ken waited until he was half way there before he moved. He walked towards Shinji and the girl, and as loud as he could said, "Well, if it isn't Shinji Ikari. I swear it's been ten years since I saw you last! What have you been up to?"

Shinji was startled to hear Kensuke's voice, that much was apparent to the young agent just from sight. Ken moved his eyes slightly up, keeping the approaching agent in his sight. Ken's outburst had also awakened the girl that was sleeping in Shinji's lap. She clung to Ken's old friend tightly as she saw him. What he heard from the girl as she held on only made Kensuke more certain they needed help.

"Is he one of the bad men, Papa?" she asked, the fear obvious in her young voice.

"No sweetheart, he's an old friend of Papa's," Shinji said, looking relieved to see the former hackers face. Indeed, it looked as if he was glad to see anyone he could trust here at all.

"That's right, knew the old man for the longest time. Kind of wondering where you've been though, and where you found such a lovely young lady to travel with," Ken said, smiling as happily as he could. The agent he had been watching had decided to wait for the time being. So Kensuke took this opportunity to sit down on Shinji's right.

Kensuke got his first good look at the kid at this point. She had brown hair, green eyes, and resembled Shinji slightly. She couldn't have been any older then three years by now. Kensuke took a seat on Shinji's right, closest to the end of the bench. Shinji was visably shaken though, more then Kensuke had expected.

"So, are you going to introduce me?" Ken prompted.

"Of course. Mana, this is Kensuke. He's a friendly person, not like the bad people. Ken, this is my daughter, Mana," Shinji said, his eyes going around a bit as he spoke. Ken thought that the young man before him may have been looking for any of the aforementioned "Bad People."

At this point Kensuke decided he'd try to get the message across to Shinji that he was in fact in danger. He hoped he'd pick up on the hint, and also hoped that Misato and Asuka would figure out what he was saying over the com he had left open before this.

--

Misato and Asuka had been listening in over the frequency Section-2 used to communicate between operatives and headquarters. They had arrived and parked across from the station about two minutes ago, not entering until they had more info. Commander Ikari had updated them on the situation, so now all they could do was wait. Misato had full confidence in Kensuke's abilities when it came to this sort of thing. She had trained him herself.

That Shinji had fathered a child had thrown the two women off guard. Misato because she had never pegged him for the type to let anyone close enough to even get into bed let alone have a child with. But for Asuka it was because he had found someone he felt comfortable enough with. She had dated on and off for the last ten years, but except for a few one night stands she hadn't really found anyone to concern herself with.

Kensuke said something over the radio just then, "Yeah, I pretty much have to go from one end of the city to the other almost twice daily. North and south, that's how it usually goes."

"Two agents on the north and the south side of the station. That pretty much means Shinji couldn't run either way to get out of there. Asuka, take the north side, I'll take the south side. The other agents should be able to assist us when the shooting starts."

"Lets just hope it doesn't, there are still a lot of civilians in there," Asuka said before they both left the car. Both women drew their weapons as they headed towards the station, hoping to avert a disastrous reunion.

--

"I'm glad to hear every thing's going so well for you Kensuke," Shinji said. He kept looking around the station though, as if he was afraid of something. Kensuke got the feeling that Shinji didn't want the attention he was drawing towards them. That made sense, Shinji never did like being the center of attention. Ken however decided it would be best to draw as much attention towards them as possible. That way if something did happen there would be plenty of witnesses.

He saw a slight refection in his glasses, the black suit who had been approaching had finally made his way behind them.

"Yeah, working at your fathers company isn't so bad. Got an office on the second floor, see Misato and Asuka on a daily basis, all in all things couldn't be better."

"Father's company?" Shinji asked, confused for a second. The look on Kensuke's face was still relaxed and laid back. But there was something in his eyes that told Shinji something. His eyes were extremely serious.

It was this time the Man in Black stopped, standing right behind them. His voice was cold when he spoke, "Shinji Ikari. By order of the UN I am to take you into custody and escort you to NERV."

Before Shinji could turn Kensuke got up and faced the other man. He smiled as he looked at the agent. His appearance and manner screamed Section-2, but Kensuke knew better. His voice didn't betray anything as he spoke, "Well, so we got a Section-2 spook. What are the odds. I suppose you wouldn't mind showing your identification. You can never be to careful these days, know what I mean?" Ken said. He glanced at Shinji slightly as he said the last part.

Shinji still wasn't sure what was happening. He had expected a Section-2 Agent to come here as soon as he called the emergency number. Why was Kensuke making so much of a fuss? Then a few things started to piece together in his brain. Things Kensuke had just said. His father's company, the second floor, and Misato and Asuka. Kensuke was the Section-2 Agent he was expecting. Which meant that this other guy was one of the men that had been chasing him and Mana the past month. Apparently he hadn't thrown them off as well as he had hoped.

"I don't have to show you anything," the Agent told Kensuke. He pulled his coat open displaying his firearm trying to send a message to the young man.

"Or really? Then you don't know about regulation 36-2903 of the NERV Section-2 SOP?" Ken asked.

"There is no such regulation. Now step aside," the agent said and made a move to grab Shinji.

He didn't expect to have his wind taken when Kensuke slammed his fist into his gut. Five seconds later he was on the floor face down as Kensuke pulled his arms behind his back and slapped on a pair of handcuffs. As he did he said, "Of course there is. 36-2903 states specifically how a Section-2 operative will dress and act when on duty. Any real Section-2 agent would know that."

Shinji was standing now holding Mana tightly. She had grabbed onto him as the other man had tried to reach for them and now held on to her father terrified. Shinji looked up and saw four more of the agents at the exits. Two had started moving towards them as Kensuke finished securing the other.

"So, I take it you have a plan for getting us out of here?" Shinji asked.

"You could say that. Anno, Sadatmo, now!" Ken said, the last into his radio. Suddenly two other people drew weapons and blocked the way of the two coming to the aide of their associate. The other two started moving, but stopped when both heard the sound of a gun being primed at the back of their heads. Shinji could see the faces of the two women that had meant so much to him during the Angel war look back at him. He could swear that Asuka had just winked at him.

For the first time since his run had began, Shinji felt as if they would be safe in this place.

--

Section-2 had sealed the area almost immediately. The five agents had been taken in for questioning. If they had any useful information the interrogators would get it out of them. If they ever saw the light of day again however was another question. Kensuke stood next to Shinji and Mana as his associates finished the clean up. He looked at his old friend and smiled.

"You have a lot to explain mister, but I'll save the catching up for later. You can tell me all about it over a nice bottle of saki," Kensuke said, his voice full of mirth.

"Not going to hound me for the gruesome details are you?" Shinji asked.

"Who me? I out grew that a long time ago. Besides, why should I spoil Misato and Asuka's fun?" Kensuke asked. The two were heading right over to them, and Kensuke figured he'd be better off in the transport with his colleagues.

"I am not looking forward to this," Shinji said.

"Comes with the homecoming, just be glad that the Commander won't be as probing as those two will be," Kensuke said, moving to leave. Before he did though he grabbed Shinji into a tight hug.

"It's really good to see you again," he said.

"You too. You're buying the drinks."

Kensuke laughed at that, then just went on his way as Misato and Asuka both ran up to Shinji. Mana was scared by the two women and just hid behind Shinji's legs, holding on tight. Shinji looked down and run his hand over her head. He tried to calm her as much as he could before he found himself locked in an extremely tight embrace.

"Shinji!" Misato practically squealed as she squeezed the life out of him. He returned the hug as best he could.

"It's been a while hasn't it Misato," he said.

"Too freakin' long if you ask me! Which you haven't yet moron," Asuka said, trying to sound angered but with a smirk on her face that said different. Misato let Shinji go and backed away, getting a good look at him.

Gone now was the thin reedy frame, now grown into a respectable medium build. He looked as if he hadn't shaved in a few days, and his face had lost much of the childlike innocence that had been robbed from him much earlier in life. He bent down and picked up Mana and held her in his arms as he said, "Mana, I want you to meet Misato and Asuka."

"Hello Misa... Misa... Misao and As... As... Assa,"Mana said, trying to say the women's names.

"Hey there, nice to meet you," Misato said, smiling at the cute little child. Both her and Asuka left the questions about the girl and her mother for later. They could tell that the child did not want their attention on her as she held her father tightly and hide her face. Shinji just held her as well, thankful that they seemed like they would be safe for now.

"Come on, lets get back to headquarters. The Commander will want to know you two are safe," Misato said. She noticed Shinji hadn't reacted to that, as if he wasn't afraid to confront his father.

Asuka hadn't said much, she just smiled as she followed the two to the old Renault Alpine. There were a thousand questions going through her head at that point. She would probably need to find a chance to get Shinji alone to herself to ask many of them. However, she had two major questions that needed to be answered. What had driven the two here, to Tokyo-03? And whom had been chasing them every step of the way?

Any further musing on Asuka's part was cut off by the distinct sound of a submachine gun's comments from outside. "Shit," she whispered to herself. "Shinji, come on, we have another escape route planned out, follow... me?" Her voice trailed off as she turned to find that Shinji and his daughter had pulled another fast fade and were nowhere to be seen.

"Misato!"

"I know, I know, but for now we have to help Kensuke and secure those prisoners, come on!" Misato told the girl as she flicked of the safety on her hand gun.

"But Misato, we can't just abandon him!" Asuka replied, anger rising in her voice.

"I know, but if we don't deal with this, will he ever be safe?"

Asuka glared at the older woman, and with a sigh of defeat took out her pistol as well. "Let's go."

With a nod, Misato took off towards the sound of gun fire, skidding to a halt by the station door and quickly looking around the corner as Asuka got behind her. "It looks like three men with HK's and another driving a sedan across the street. Ken is pinned down and Sadatmo is down. I didn't see Anno, but he might be keeping the prisoners under control in the van."

"Right, what's the plan?"

"I'll lay down some cover fire, and you get to the front of the van where the shot guns are. After that, it's the basic 'put holes in the other guy' stratagem."

"Got it, Misato," Asuka said as she prepared herself to run across the parking lot to the van. "Ready when you are."

"GO!" Misato yelled as she broke cover and began to fire on the men at the car. She had a lucky angle, and the cover that the sedan was providing from Kensuke didn't help as much against her. Her first rounds caught one of the assailants in his shoulder and with a scream he spun, dropping his weapon. One of the others quickly redirected and began to fire in Misato's direction as she ducked back behind cover to put in a fresh clip. Seized by a sudden inspiration, she quickly judged the weight of her spent clip before rounding the corner and screaming "FIRE IN THE HOLE" threw it at the enemy gunmen, sending a spray of bullets after. The two standing gunmen dove for cover as the spent clip bounced off the hood of their car, for a moment, too occupied to return fire.

Asuka had taken of running as soon as Misato had told her, firing a few shoots blindly towards her assailants. She had almost covered the distance to the safe cover of the van when a stray shot clipped her arm. Despite the flash of pain, she was able to roll to cover, but not close enough to the van's front door. "What happened?" she asked Kensuke as she stood up and prepared to make a bolt for the van's closed passenger door.

"I don't know, the bastards came out of nowhere, and gunned down Sadatmo right after Anno got the prisoners loaded into the van. Anno's keeping them covered. I think the only reason they haven't advanced yet is because they don't know how many of us are here."

Kensuke might have said more except that he was interrupted by Misato's warning of an active explosive. While the Section 2 agent ducked behind the cover of the van, Asuka grinned and made her run for the vans door as the two remaining gunmen dove for cover. Asuka threw open the door and reached behind what some American friends often called the 'shotgun seat' and drew forth its namesake. "Ken!" she shouted as she tossed the heavier weapon to the agent, who ducked around the corner long enough to catch it. Asuka drew another 12 gauge as the assailants recovered and she began to let lose with the weapon as Kensuke rounded the corner and let lose as well.

As shotgun rounds began impacting on the sides and hood of the sedan, the two standing gunmen pulled in their fallen comrade and the car speed away as Kensuke unloaded a few more rounds at the cars fleeing taillights.

"Damn, they're gone," Misato said as she looked into the now deserted transit station.

Kensuke walked up to the two women and looked into the station as well. "Back up's on the way. You two go look for them, Anno and I will keep the prisoners under control."

Asuka and Misato ran to the car, the doors slamming as Misato gunned the engine and went off into the city. Asuka was reaching for the radio to put out an all points bulletin out for the two when Misato switched it off. Asuka gave Misato a look and understood immediately. Somehow, the team at the station had known they would be there, and brought the fire power to deal with it.

"So, where do we start looking?" Asuka asked.

"The only place that makes sense," Misato answered.

"Makes sense? He could be anywhere, The city is huge and he knows every hiding place there is. Where could we possibly go without getting help from Central?"

"Home," Misato said, gunning the engine hard on the street.

--

Kensuke opened the transport after they had arrived at NERV to allow the prisoners to be escorted to the lower holding cells. The interrogation would have to start shortly, should any information they had become useless. That would not be of any help to him or anyone else trying to keep Shinji and his daughter alive. What he saw when he opened the door was not a good sign.

The five agents were all laying in the transport, blood dripping out of their mouths. Checking each of them he found all had died in transit. They would not be speaking to anyone now, protecting whoever it was that had sent them. All Kensuke could do was curse under his breath as the bodies were removed from the transport. Hopefully medical would be able to tell them what had caused these deaths.

This was starting to smell of something much darker then anyone could imagine, of this Kensuke was certain.

To Be Continued...

Authors Notes: Hello all! Just couldn't help myself when this idea came to mind. Well, looks like the bug has bitten into me yet again. The problem here is focusing on how much of Original Shinji and how much Extra Crispy to put into the mix. But I assure you this will be a kick ass story when it's done. :-D At least I think it will be.

Next Chapter: Reunions and introductions follow, as Shinji and Mana set up house with Misato and Asuka. Some friends old and some new are brought to bare as the two finally have a chance to deal with the lose that drove them here. And a reunion as feared as it was inevitable brings new light to an old hurt.

But the agents of some darker conspiracy lurk, and have their eyes set on the one last thing Shinji cares about in the world.

Next Chapter: Racing Tokyo-3

Prereaders – MasterChief, Isamu


	2. Racing Tokyo3

Run

Chapter 2: Racing Tokyo-3

An Evangelion Fanfiction

By: Legato Deathscythe

Misato drove fast through the streets of Tokyo-3. The emergency transponder in her car tracked her through the city, notifying any public authorities she may have passed that she was on official business and not to be stopped. Asuka held onto the handle that was attached to the passenger side above the door. This was not unusual in itself, however now it wasn't simply out of fear for her life.

"Are you certain he would head there? He doesn't know if we moved out or what happened since he left? Hell, he could be hiding in any number of places, and he has always been very gifted when it comes to hiding," Asuka said as Misato took a rather sharp turn.

"He wants to be found this time. And even with those guys who showed up at the station we have to assume he's come here intending to be found at least by us. He'll go to the one place he knows we will look but no one else would think of," Misato said.

"Can he even get in and out of sight?"

"I never changed the locks."

--

Misato and Asuka approached the door to their apartment. Each of the women drew their sidearm when they saw the door was slightly ajar. Slowly they made their way into the apartment, covering every inch of the place as they could. Pen-Pen, older and slightly graying now, walked forward with a beer in his flipper. He looked over the two and waved his free flipper indicating they should follow him. The old bird led them to a long since abandoned room down the hall, where inside they found a touching if sad sight.

Shinji had lain down on his old bed, fast asleep with his daughter sleeping soundly on his chest.

--

Kensuke had been called to the Commander's Office immediately after they had arrived at NERV Central. That his captives had died in route did not fill him with confidence that this summons would turn out well for him. If he was lucky, he'd probably only get a reprimand. He didn't want to think about how it could be worse.

He stood before the Commander and Sub-Commander as he delivered his report on what had happened in the Transit Station. He remained calm and collected, giving the precise details as well as he could. When he finished he stood there waiting for the Commander to ask any questions.

"So, they died in transit?" Ikari asked.

"Yes sir. Preliminary report from the coroner indicates that they died from a major aneurysm in the cerebral cortex. The blood vessels in their brains just burst."

"And you have no idea how this was caused," The Commander said, it was not a question.

"No sir. I've not heard of anything similar to this. We originally searched them to make sure they weren't carrying any extra weapons or toxic agents. Our search found nothing to point towards a cause."

Gendo sat his chin in his hands and took the Agent's appearance in. No one would have thought their prisoners would blow their own brains from the inside. He would not hold Aida responsible for this event. In fact, he had something else in mind.

"You have performed admirably in this situation Agent Aida. As such I am issuing orders to promote you to lieutenant effective immediately. Your first task in your new position will be to take control of this investigation and coordinate security for the Third Child and his daughter," Commander Ikari said.

If Kensuke was annoyed that the Commander hadn't used Shinji's name, he didn't show it. He was actually relieved that he hadn't been punished for this, in fact promoted instead. First thing was to begin the investigation, starting with Shinji.

"Thank you sir. I'll begin arraigning to question Shinji as soon as possible," Kensuke said. What came next he didn't quiet expect.

"No, I shall question him," the Commander said.

Kensuke didn't ask for an explanation, that would not do under any circumstances. He merely asked, "Do you want me to have him brought here sir?"

"No. Wait two hours, give him enough time to eat and rest for a moment. Then take him to the Eva holding cages. Cage One specifically."

Kensuke knew full well what was in Cage One, everyone in NERV did. He didn't question his orders though, he simply said, "Yes sir."

After Aida had been dismissed Gendo stood and went to the observation window looking out over Cage One. Fuyutsuki came up behind him and asked, "Why do you want to talk with him there?"

All Gendo could say was, "Family reunion."

--

Shinji had never liked being in the Geo-front Too many nightmares were buried in the vast underground, some that haunted him even as the car train descended into the chasm. Mana hadn't noticed having fallen back to sleep against him as Misato drove. He ran his fingers through her hair. This was the only peace she found these days. All he could hope for was that there would be light at the end of this dark tunnel for the both of them.

So wrapped up in hope and worry about their immediate future, Shinji hadn't noticed Asuka glancing at him from time to time using one of the rear view mirrors. She kept staring at the pair, just watching them. In a way she was happy, happy her one time comrade had found something worth living for. She was also slightly jealous of the Third Child. He had found that thing she had not even glimpsed a hint of yet in her life. Asuka decided she would do what she could to preserve the last bit of that for him. She was too busy thinking to notice Misato glancing at her from time to time.

The car continued it's long decent to the floor of the Geo-front in silence.

--

Misato had taken Shinji and Mana to one of the VIP lounges in the upper levels of the complex. She had had a small meal brought up from the cafeteria for the two, and had watched them as they had eaten. The young girl ate timidly, not quiet enjoying being watched by the woman she didn't know. When she finally finished she pushed her plate away and then looked to her father who was on one of the lounge couches.

She got out of her seat and walked over to him. She climbed up and held onto one of Shinji's arms while burying her face into his chest. Shinji didn't say anything, just wrapped his arm around his daughter. The young man held his daughter close, and for a moment closed his eyes as they both sat there. It was a heartwarming scene to Misato.

Shinji looked exhausted, as if he hadn't really slept for a long time. Misato couldn't imagine what he had been through the past ten years. She didn't even have the first clue about what had driven them there. But the fact that five hostiles had been waiting for them dressed as NERV personnel meant that someone high up on the food chain wanted them. The team that had shown up as back up only acted to accentuate this point. She didn't want to disturb the two, but Misato needed answers.

She however would have to wait, as Kensuke entered the lounge and approached her. "Well, that was interesting."

"What Commander Ikari have to say?" Misato asked.

"Well, he went over the report. I don't think I've seen him as interested in anything as long as I've worked here. He's requested I take Shinji down to Cage One in about an hour. Commander Ikari intends to do the initial questioning personally. Don't ask me why, you'd know better then I would," Kensuke said. Asuka walked over to them as all three kept watch over the pair.

Kensuke asked what they were all thinking, "What do you think her mother was like?"

Neither woman could answer him.

--

Shinji wasn't comfortable leaving his daughter right now. However he didn't want her to be there when he met his father again, in case it didn't go well. Misato and Asuka readily agreed to watch Mana for him while Kensuke took him to the cages. Fitting, his father was not without a sense of irony. After they had arrived Ken had stepped out into the corridor, to maintain security he said. Shinji thought he didn't want to have to be the one to shoot Shinji if he attacked the Commander.

Not that he would.

Shinji stood upon the walk way, his eyes glued to the repaired hulk that he had known as Unit-01. It had been completely repaired, right down to the paint on the armor. Shinji had not expected it to be in this kind of shape, even in one of NERV's cage areas. If anything, after Third Impact he had expected Unit-01 to have been lost in the Eva Graveyard deep within Terminal Dogma. To see the monster of his past standing before him yet again was unsettling to say the least.

"I sometimes ask myself, is she still in there," a voice said from behind him. Shinji turned around to see his father walking up beside him. The years had turned his fathers hair stone gray along the sides, and had etched out lines along his eyes and face. He walked slower then Shinji remembered, however he retained the same confidant stride Shinji remembered.

"For all I know, your mother could still be inside Unit-01's core. The only way to find out would be to put someone in the pilot's chair. I'm too afraid to try though. If she is there, then I would know that there was no way for her ever to be freed from it. And if she isn't, then I would have another person's blood on my hands when Unit-01 took them into herself."

Gendo set his hands on the railing, the black glove on his right hand unmistakably present. He stared into Unit-01's eyes for a moment, than turned to Shinji. His eyes scanned the boy he had considered over the years many things. He now saw something he had come to understand just after his plans had failed. He saw himself in his son's eyes, his son's face. But also, Gendo saw Yui in his son's heart. The way he protected the girl left no doubt of that.

"It's been a while, hasn't it," Gendo said.

"That was the first thing you said to me before putting me in Unit-01 all those years ago," Shinji said, finding it difficult to meet Gendo's eyes.

"Very true, I felt this was an appropriate place for a reunion, considering. You, me, your mother if she's even in there, you'd know that better then I would though. A small family reunion that we really never had the chance for until now. Granted I think we can both agree that it would be sweeter if the events of the last twenty years hadn't occurred and the three of us had been left to be a family."

"We weren't given that chance, and I would think by now you knew you couldn't raise the dead."

"True, very true," Gendo replied. The older man took a deep breath and released it. "I've spent the last ten years keeping as many people as I could off your tail. It seems I have failed even in that. My sources are trying to find out who it is that is and why the seem willing to risk what I might do."

Shinji nodded at that. He stared into the behemoths eyes, trying to see if there was anything left in there of his mother. He had always felt something, even before he learned the truth. It always felt like she was with him, especially after the Fourteenth. He looked into the eyes of Unit-01 just as they flashed at him with recognition.

"She is there, watching us. I think she has unfinished business before she can truly be free of this thing," Shinji said.

Gendo nodded, disturbed by how easily the young man had seen into that. Gendo however had a feeling he knew what she wanted to see. After all, he needed it to happen as much as Yui would want to see it.

"I know I caused you much pain over the years. Too much to be forgiven, but that is the past. I promise I will use every resource I have available, every contact at my disposal, to ensure that you and your daughter are safe," Gendo said.

Shinji nodded, "I know you will. I forgave you of most everything a long time ago. The rest, well when Yukio was killed I understood everything else after that. I was so tempted to send Mana somewhere away from me to keep her safe."

Gendo nodded again. He placed his hand on his son's shoulder and squeezed. Shinji turned and looked into his father's eyes. "Tell me about my granddaughter and her mother Shinji."

As they talked Unit-01 watched, it's eyes following the two as they spoke truly as father and son for the first time.

--

It was later that night when Misato, Asuka, Kaji, Kensuke, and Fuyutsuki sat in one of the conference rooms in the upper levels the pyramid. Shinji and Mana had been shown to guest quarters where a full Section-2 detail stood watch over them. Kaji had been working his contacts over hard ever since the initial incident, while Kensuke had looked over medicals preliminary report on the agents bodies.

Asuka and Misato had not left Shinji's side since his return from speaking with his Father. Oddly enough to the two he seemed a bit happier then when he left. His improved mood was contagious. Mana had begun to seem more like the happy child the two thought she should be. Asuka had even brought her a doll to play with while Shinji showered.

Commander Ikari joined them shortly and started the meeting, "What have we been able to find out?"

Kensuke answered first, "Medicals preliminary findings suggest that the prisoners deaths were caused by an implanted device that was activated through a switch in the jaw. They've not seen anything like this. The coroner is consulting with MOI, INTERPOL, JSSDF, CIA, MI-6, and UN intel to see if they know of anything similar."

"So far none of my contacts have been able to give me any information on the identities of our mystery assailants. I did get a call though just before the PID came in, seemed that specific contact wanted to be kept appraised of a fugitive and his daughter. It's too coincidental for me not to ignore," Kaji said.

Misato was already beginning to feel annoyed, "Did he say why?"

"Only that JSSDF intel and MOI had been watching their fugitive for some time. I'm still digging though," Kaji said. He and the Commander both knew what this might mean. Ikari was already preparing to have a talk with certain people.

"So for now we know little more then he is being hunted, possibly by the JSSDF and others," Commander Ikari said.

There were nods around the table. Asuka asked the question on all their minds, "What do we do?"

Ikari had an answer already, "For now all information concerning his whereabouts is strictly confidential. Only those who need to know or can be trusted will have any access. Until we can provide secure housing keep them both in the Geo-Front with access outside headquarters but not to the surface at this time. I want to ensure we can get more information without risking their safety."

There were nods of consent and understanding around the table. Gendo turned to Misato and Asuka, "I want you two to stay close to them and assist them as needed."

Both women nodded. Gendo turned to Kensuke and said, "Lt. Aida, I want you to continue along your line of inquiry. Also, see if you can locate any information with civilian authorities that seems close to what Agent Kaji's contact mentioned."

"Yes sir," Kensuke said.

"Dismissed," Gendo said, sending everyone on their way. He however stopped Kaji before he left, "You have other sources as well as I do. Make sure the Old Men aren't looking for a way to take some small amount of revenge against us."

"So you think Kiel may be up to his old tricks?"

"I wouldn't discount it. We never did locate and confirm kills on all the Old Men, Kiel especially. I'd rather not be caught unawares by them," Gendo said.

"I'll see what I can find," Kaji said. Before he left he turned, smirking at Gendo, "So how does it feel to be a Grandfather?"

"I'll let you know after I finally start acting like a father," was Gendo's reply.

Kaji smirked back, "I don't know. I always thought one of the things a real father did was protect their children, no matter what. Seems you're doing pretty well so far."

Kaji left Gendo to his thoughts, both men deciding they had some people to talk to that wouldn't enjoy the encounters.

–

Fuyutsuki was waiting for Gendo in his office. The old professor could barely make the long walk to the doors for the commanders office without the aid of his cane. Age and stress had etched an even more intricate set of lines and wrinkles along Fuyutsuki's face. Gendo more then understood when the man didn't get up. Gendo sat down in his chair behind the desk and said, "Someone is sniffing in places they don't belong."

"Why am I not surprised? You would think everything we've done to protect our people over the last decade would have warned everyone off," Fuyutsuki said.

"The question is who is behind all of this and what is really happening. I doubt the Old Men would try to use him to get revenge after so long, but I wouldn't put it past them," Gendo said.

"What about the UN?"

Gendo shook his head, "They have no desire to do anything of the kind either. He had no tactical significance aside from Unit-01, and he wasn't wanted for anything either."

Fuyutsuki shook his head, "We've been too complacent it seems. There could be who knows how many people who would want him or his child that we don't know about."

Gendo merely nodded, "We will have to use what resources we can to smoke this new player out."

Fuyutsuki shook his head as he slowly stood up, "I'm afraid you'll have to do so without me, old friend. I'm much too old for this game. Hell, I was old when we went against the Angels and Seele. It's time I finally retire."

Gendo didn't let his shock show. He stood respectfully and understandingly said, "I appreciate you staying with us for as long as you could, Professor."

Kozo smirked, "I'll keep the Shogi board ready."

The two men shook hands, and Kozo left Gendo Ikari's office for the last time. Gendo leaned into his desk, his hands joining in front of his chin as he rested on them. He had taken this pose to intimidate, think, and typically observe things. It was fitting that now, as he considered the future of certain people under his protection he should return to this familiar pose.

"_A viper in the bushes, waiting to strike us when we least expect it,"_ was his only thought as he sat there.

To Be Continued...

Authors Notes: I think this works. Had a big disagreement with datdude on Shinji forgiving Gendo, but I decided to stick with it as I had. I just don't see Shinji as the type to hold a grudge, ever.

FFN Notes: A New Chpater of Forgotten Warriors is almost ready. Keep an eye on it. Also there is a new poll up on the profile. Check it out and vote. As always reviews are requested, of all types. And if you have never read or reviewed my other works please do so. I could use the fresh perspective on some of them.

Check the FFN and DS forums, I could always use the feedback.


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